have you looked at the MSDOS era Master Of Orion 1 and 2, cant speak much for 1 as I haven't played it but the only things lacking between MOO2 and SotS from your list are:
Realtime space combat (it's turn based in MOO2), though the Total War franchise does deal with RTS combat resolution,
drop in/out multi because there wasn't the market for it in multiplayer back in the 90's,
differing FTL methods.
research driven ship customization
Master of Orion has a much more flexible modification system, which also takes into account tech miniaturisation from improving tech levels. Alpha Centauri also features significant unit customisation.
Not only that but MOO2 has a much more restrictive research tree, want fusion FTL, fine but you cant have fusion missiles, you can if want to choose/customise a race that turns it off but it will come with some pretty big penalties.
Scale, yes the game take advantage that the more modern computer memory can hold larger arrays to store more systems.
anyhow there is a saying in fiction, "it's all been done before". Meaning a genuinely unique idea is very rare and while the differing FTL is not something I have come across before in a 4X, and several aspects of SotS is uncommon as is how it combines many aspects but it is sadly not all that new, just presented with more modern graphics.